Peptide and protein analysis

Thermo Fisher Scientific has published an application note that illustrates the capabilities of dual-pressure, linear ion trap technology for the investigation of proteome dynamics.

The application note assessed the performance of the LTQ Velos ion trap mass spectrometer for the analysis of a complex, multi-organ peptide digest of Caenorhabditis elegans (C. elegans). The LTQ Velos ion trap mass spectrometer offers improvements in speed and sensitivity, providing greater coverage in the analysis of complex peptide mixtures and increasing the confidence of protein identification at low sample levels. The Novel Dual-Pressure Linear Ion Trap Mass Spectrometer Offers Breakthrough Performance in Proteomics Experiments note is available for download via www.thermo.com/velos462.

Tandem mass spectrometry, particularly using linear ion traps and trap-based hybrid mass spectrometers, has become a leading technology for peptide and protein identification. The preference for this technology is due to its ease of use as well as its superior MS and MS/MS performance. The multiple fragmentation techniques available on the LTQ Velos enable more confident sequence assignment and post-translational modification (PTM) identification. Faster scan rates also significantly reduce cycle times, increasing the number of proteins and peptides identified.

The application note describes an effective method for the analysis of peptides and proteins using the LTQ Velos mass spectrometer. To compare and benchmark performance, the company ran analyses on both a LTQ XL linear ion trap mass spectrometer and a quadrupole time-of-flight (Q-TOF) mass spectrometer. The study used data-dependent tandem acquisition methods and the team separated a proteolytic digest of C. elegans using reverse-phase chromatography for each LC-MS/MS run. The analysis revealed that the LTQ Velos identifies ~240% more proteins and ~130% more distinct peptides from a highly complex sample than is possible with the Q-TOF.